Keep the KEGG coordinates while passing KEGG pathway (graphNEL) to igraph
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5.1 years ago

Hello Everyone,

I downloaded the KEGG pathway using the parseKGML2Graph FUNCTION and when i plot the graph directly it shows a nice graph with KEGG coordinates, But when i convert the graphNEL object to igraph using igraph.from.graphNEL , it loses it coordinates. I want the same coordinates as KEGG graph, How can i do it ?

KEGG igraph R • 1.6k views
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Can you include some code that we can use as a minimum reproducible example? The attributes of the nodes in the graphNEL object can be obtained by getKEGGnodeData() and there (in the graphics slot for each node) you can find information like x and y coordinates. But I am not sure if that is what you are looking for.